Cosmic Era (C.E.) 73. Two years after the peace treaty between ZAFT and the Earth Alliance was signed in Mobile Suit Gundam SEED, members of the Earth Alliance special task force known as Phantom Pain hijack three advanced mobile suits from a ZAFT armoury base during a meeting between Orb representative Cagalli Yula Athha and new ZAFT chairman Gilbert Durandal. What begins as a pursuit of this band of Extended Naturals by Orb refugee Shinn Asuka, Athrun Zala, and the crew of the LHM-BB01 Minerva, escalates into cataclysmic circumstances which lead to the declaration of yet another war.

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